keyword
MENU ▼
Read by QxMD icon Read
search

genome-wide

keyword
https://www.readbyqxmd.com/read/28918587/genome-wide-association-studies-of-albuminuria-towards-genetic-stratification-in-diabetes
#1
REVIEW
Cristian Pattaro
Genome-wide association studies (GWAS) have been very successful in unraveling the polygenic structure of several complex diseases and traits. In the case of albuminuria, despite the large sample size achieved by some studies, results look sparse with a limited number of loci reported so far. This review searched for GWAS studies of albumin excretion, albuminuria, and proteinuria. The resulting picture sets elements of uniqueness for albuminuria GWAS with respect to other complex traits. So far, very few loci associated with albuminuria have been validated by means of genome-wide significant evidence or formal replication...
September 16, 2017: Journal of Nephrology
https://www.readbyqxmd.com/read/28918554/genome-wide-identification-classification-evolutionary-analysis-and-gene-expression-patterns-of-the-protein-kinase-gene-family-in-wheat-and-aegilops-tauschii
#2
Jun Yan, Peisen Su, Zhaoran Wei, Eviatar Nevo, Lingrang Kong
In this study we systematically identified and classified PKs in Triticum aestivum, Triticum urartu and Aegilops tauschii. Domain distribution and exon-intron structure analyses of PKs were performed, and we found conserved exon-intron structures within the exon phases in the kinase domain. Collinearity events were determined, and we identified various T. aestivum PKs from polyploidizations and tandem duplication events. Global expression pattern analysis of T. aestivum PKs revealed that some PKs might participate in the signaling pathways of stress response and developmental processes...
September 16, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28918100/transcriptomic-and-epigenomic-biomarkers-of-antidepressant-response
#3
REVIEW
Raoul Belzeaux, Rixing Lin, Chelsey Ju, Marc-Aurele Chay, Laura M Fiori, Pierre-Eric Lutz, Gustavo Turecki
BACKGROUND: Antidepressant treatment is associated with a high rate of poor response, and thus, biomarker development is warranted. METHODS: We aimed to synthesize studies investigating gene expression, small RNAs, and epigenomic biomarkers of antidepressant response. We conducted a narrative review of the literature. RESULTS: Firstly, we detailed the challenges involved, in terms of biological tissues, relevant study time frames, and mandatory statistical tools...
September 8, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28918050/the-function-and-therapeutic-potential-of-long-non-coding-rnas-in-cardiovascular-development-and-disease
#4
REVIEW
Clarissa P C Gomes, Helen Spencer, Kerrie L Ford, Lauriane Y M Michel, Andrew H Baker, Costanza Emanueli, Jean-Luc Balligand, Yvan Devaux
The popularization of genome-wide analyses and RNA sequencing led to the discovery that a large part of the human genome, while effectively transcribed, does not encode proteins. Long non-coding RNAs have emerged as critical regulators of gene expression in both normal and disease states. Studies of long non-coding RNAs expressed in the heart, in combination with gene association studies, revealed that these molecules are regulated during cardiovascular development and disease. Some long non-coding RNAs have been functionally implicated in cardiac pathophysiology and constitute potential therapeutic targets...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28917824/parkinson-s-disease-susceptibility-variants-and-severity-of-lewy-body-pathology
#5
Michael G Heckman, Koji Kasanuki, Nancy N Diehl, Shunsuke Koga, Alexandra Soto, Melissa E Murray, Dennis W Dickson, Owen A Ross
INTRODUCTION: Meta-analyses of genome-wide association studies (GWAS) have established common genetic risk factors for clinical Parkinson's disease (PD); however, associations between these risk factors and quantitative neuropathologic markers of disease severity have not been well-studied. This study evaluated associations of nominated variants from the most recent PD GWAS meta-analysis with Lewy body disease (LBD) subtype (brainstem, transitional, or diffuse) and pathologic burden of LB pathology as measured by LB counts in five cortical regions in a series of LBD cases...
September 11, 2017: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/28917724/backward-genotype-transcript-phenotype-association-mapping
#6
Seunghak Lee, Haohan Wang, Eric P Xing
Genome-wide association studies have discovered a large number of genetic variants associated with complex diseases such as Alzheimer's disease. However, the genetic background of such diseases is largely unknown due to the complex mechanisms underlying genetic effects on traits, as well as a small sample size (e.g., 1000) and a large number of genetic variants (e.g., 1 million). Fortunately, datasets that contain genotypes, transcripts, and phenotypes are becoming more readily available, creating new opportunities for detecting disease-associated genetic variants...
September 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28917158/quantitative-trait-locus-mapping-in-mice-identifies-phospholipase-pla2g12a-as-novel-atherosclerosis-modifier
#7
Alexandros Nicolaou, Bernd H Northoff, Kristina Sass, Jana Ernst, Alexander Kohlmaier, Knut Krohn, Christian Wolfrum, Daniel Teupser, Lesca M Holdt
BACKGROUND AND AIMS: In a previous work, a female-specific atherosclerosis risk locus on chromosome (Chr) 3 was identified in an intercross of atherosclerosis-resistant FVB and atherosclerosis-susceptible C57BL/6 (B6) mice on the LDL-receptor deficient (Ldlr(-/-)) background. It was the aim of the current study to identify causative genes at this locus. METHODS: We established a congenic mouse model, where FVB.Chr3(B6/B6) mice carried an 80 Mb interval of distal Chr3 on an otherwise FVB...
September 4, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28916929/trace-elements-and-healthcare-a-bioinformatics-perspective
#8
Yan Zhang
Biological trace elements are essential for human health. Imbalance in trace element metabolism and homeostasis may play an important role in a variety of diseases and disorders. While the majority of previous researches focused on experimental verification of genes involved in trace element metabolism and those encoding trace element-dependent proteins, bioinformatics study on trace elements is relatively rare and still at the starting stage. This chapter offers an overview of recent progress in bioinformatics analyses of trace element utilization, metabolism, and function, especially comparative genomics of several important metals...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28916820/accumulation-of-minor-alleles-and-risk-prediction-in-schizophrenia
#9
Pei He, Xiaoyun Lei, Dejian Yuan, Zuobin Zhu, Shi Huang
Schizophrenia is a common neuropsychiatric disorder with a lifetime risk of 1%. Accumulation of common polygenic variations has been found to be an important risk factor. Recent studies showed a role for the enrichment of minor alleles (MAs) of SNPs in complex diseases such as Parkinson's disease. Here we similarly studied the role of genome wide MAs in schizophrenia using public datasets. Relative to matched controls, schizophrenia cases showed higher average values in minor allele content (MAC) or the average amount of MAs per subject...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916739/a-moso-bamboo-wrky-gene-pewrky83-confers-salinity-tolerance-in-transgenic-arabidopsis-plants
#10
Min Wu, Huanlong Liu, Guomin Han, Ronghao Cai, Feng Pan, Yan Xiang
The WRKY family are transcription factors, involved in plant development, and response to biotic and abiotic stresses. Moso bamboo is an important bamboo that has high ecological, economic and cultural value and is widely distributed in the south of China. In this study, we performed a genome-wide identification of WRKY members in moso bamboo and identified 89 members. By comparative analysis in six grass genomes, we found the WRKY gene family may have experienced or be experiencing purifying selection. Based on relative expression levels among WRKY IIc members under three abiotic stresses, PeWRKY83 functioned as a transcription factor and was selected for detailed analysis...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916648/genome-dynamics-of-hybrid-saccharomyces-cerevisiae-during-vegetative-and-meiotic-divisions
#11
Abhishek Dutta, Gen Lin, Ajith V Pankajam, Parijat Chakraborty, Nahush Bhat, Lars M Steinmetz, Koodali T Nishant
Mutation and recombination are the major sources of genetic diversity in all organisms. In the baker's yeast, all mutation rate estimates are in homozygous background. We determined the extent of genetic change through mutation and loss of heterozygosity (LOH) in a heterozygous Saccharomyces cerevisiae genome during successive vegetative and meiotic divisions. We measured genome wide LOH and base mutation rates during vegetative and meiotic divisions in a hybrid (S288c/YJM789) S. cerevisiae strain. The S288c/YJM789 hybrid showed nearly complete reduction in heterozygosity within 31 generations of meioses and improved spore viability...
September 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28916647/the-effect-of-common-inversion-polymorphisms-in-2l-t-and-in-3r-mo-on-patterns-of-transcriptional-variation-in-drosophila-melanogaster
#12
Erik Lavington, Andrew D Kern
Chromosomal inversions are an ubiquitous feature of genetic variation. Theoretical models describe several mechanisms by which inversions can drive adaptation and be maintained as polymorphisms. While inversions have been shown previously to be under selection, or contain genetic variation under selection, the specific phenotypic consequences of inversions leading to their maintenance remain unclear. Here we use genomic sequence and expression data from the Drosophila Genetic Reference Panel to explore the effects of two cosmopolitan inversions, In(2L)t and In(3R)Mo, on patterns of transcriptional variation...
September 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28916644/subset-and-tissue-defined-stat5-thresholds-control-homeostasis-and-function-of-innate-lymphoid-cells
#13
Alejandro V Villarino, Giuseppe Sciumè, Fred P Davis, Shigeru Iwata, Beatrice Zitti, Gertraud W Robinson, Lothar Hennighausen, Yuka Kanno, John J O'Shea
Innate lymphoid cells (ILCs) patrol environmental interfaces to defend against infection and protect barrier integrity. Using a genetic tuning model, we demonstrate that the signal-dependent transcription factor (TF) STAT5 is critical for accumulation of all known ILC subsets in mice and reveal a hierarchy of STAT5 dependency for populating lymphoid and nonlymphoid tissues. We apply transcriptome and genomic distribution analyses to define a STAT5 gene signature in natural killer (NK) cells, the prototypical ILC subset, and provide a systems-based molecular rationale for its key functions downstream of IL-15...
September 15, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28916551/genetic-determinants-of-radiographic-knee-osteoarthritis-in-african-americans
#14
Youfang Liu, Michelle S Yau, Laura M Yerges-Armstrong, David J Duggan, Jordan B Renner, Marc C Hochberg, Braxton D Mitchell, Rebecca D Jackson, Joanne M Jordan
OBJECTIVE: The etiology of knee osteoarthritis (OA), the most common form of arthritis, is complex and may differ by race or ethnicity. In recent years, genetic studies have identified many genetic variants associated with OA, but nearly all the studies were conducted in European whites and Asian Americans. Few studies have focused on the genetics of knee OA in African Americans. METHODS: We performed a genome-wide association study of radiographic knee OA in 1217 African Americans from 2 North American cohort studies: 590 subjects from the Johnston County Osteoarthritis Project and 627 subjects from the Osteoarthritis Initiative...
September 15, 2017: Journal of Rheumatology
https://www.readbyqxmd.com/read/28916491/controversy-and-debate-on-clinical-genomics-sequencing-paper-2-clinical-genome-wide-sequencing-don-t-throw-out-the-baby-with-the-bathwater
#15
Shelin Adam, Jan M Friedman
Genome-wide (exome or whole genome) sequencing with appropriate genetic counselling should be considered for any patient with a suspected mendelian disease that has not been identified by conventional testing.Clinical genome-wide sequencing provides a powerful and effective meansof identifying specific genetic causes of serious disease and improving clinical care.
September 12, 2017: Journal of Clinical Epidemiology
https://www.readbyqxmd.com/read/28916376/transcriptome-profiling-of-the-plutella-xylostella-lepidoptera-plutellidae-ovary-reveals-genes-involved-in-oogenesis
#16
Lu Peng, Lei Wang, Yi-Fan Yang, Ming-Min Zou, Wei-Yi He, Yue Wang, Qing Wang, Liette Vasseur, Min-Sheng You
BACKGROUND: As a specialized organ, the insect ovary performs valuable functions by ensuring fecundity and population survival. Oogenesis is the complex physiological process resulting in the production of mature eggs, which are involved in epigenetic programming, germ cell behavior, cell cycle regulation, etc. Identification of the genes involved in ovary development and oogenesis is critical to better understand the reproductive biology and screening the potential molecular targets in Plutella xylostella, a worldwide destructive pest of economically major crops...
September 12, 2017: Gene
https://www.readbyqxmd.com/read/28916367/rucaparib-maintenance-treatment-for-recurrent-ovarian-carcinoma-after-response-to-platinum-therapy-ariel3-a-randomised-double-blind-placebo-controlled-phase-3-trial
#17
Robert L Coleman, Amit M Oza, Domenica Lorusso, Carol Aghajanian, Ana Oaknin, Andrew Dean, Nicoletta Colombo, Johanne I Weberpals, Andrew Clamp, Giovanni Scambia, Alexandra Leary, Robert W Holloway, Margarita Amenedo Gancedo, Peter C Fong, Jeffrey C Goh, David M O'Malley, Deborah K Armstrong, Jesus Garcia-Donas, Elizabeth M Swisher, Anne Floquet, Gottfried E Konecny, Iain A McNeish, Clare L Scott, Terri Cameron, Lara Maloney, Jeff Isaacson, Sandra Goble, Caroline Grace, Thomas C Harding, Mitch Raponi, James Sun, Kevin K Lin, Heidi Giordano, Jonathan A Ledermann
BACKGROUND: Rucaparib, a poly(ADP-ribose) polymerase inhibitor, has anticancer activity in recurrent ovarian carcinoma harbouring a BRCA mutation or high percentage of genome-wide loss of heterozygosity. In this trial we assessed rucaparib versus placebo after response to second-line or later platinum-based chemotherapy in patients with high-grade, recurrent, platinum-sensitive ovarian carcinoma. METHODS: In this randomised, double-blind, placebo-controlled, phase 3 trial, we recruited patients from 87 hospitals and cancer centres across 11 countries...
September 12, 2017: Lancet
https://www.readbyqxmd.com/read/28915899/association-between-polymorphisms-of-tas2r16-and-susceptibility-to-colorectal-cancer
#18
Jonathan Barontini, Marco Antinucci, Sergio Tofanelli, Maurizio Cammalleri, Massimo Dal Monte, Federica Gemignani, Pavel Vodicka, Roberto Marangoni, Ludmila Vodickova, Juozas Kupcinskas, Veronika Vymetalkova, Asta Forsti, Federico Canzian, Angelika Stein, Victor Moreno, Nicola Mastrodonato, Francesca Tavano, Anna Panza, Roberto Barale, Stefano Landi, Daniele Campa
BACKGROUND: Genetics plays an important role in the susceptibility to sporadic colorectal cancer (CRC). In the last 10 years genome-wide association studies (GWAS) have identified over 40 independent low penetrance polymorphic variants. However, these loci only explain around 1‑4% of CRC heritability, highlighting the dire need of identifying novel risk loci. In this study, we focused our attention on the genetic variability of the TAS2R16 gene, encoding for one of the bitter taste receptors that selectively binds to salicin, a natural antipyretic that resembles aspirin...
September 15, 2017: BMC Gastroenterology
https://www.readbyqxmd.com/read/28915836/changes-in-dna-methylation-in-na%C3%A3-ve-t-helper-cells-regulate-the-pathophysiological-state-in-minimal-change-nephrotic-syndrome
#19
Yasuko Kobayashi, Akira Aizawa, Takumi Takizawa, Katsuhide Igarashi, Izuho Hatada, Hirokazu Arakawa
BACKGROUND: DNA methylation plays a crucial role in regulating transcription, and changes in DNA methylation affect gene expression and disease development. Minimal change nephrotic syndrome (MCNS) has been reported to involve immunological disturbances. Since the characteristic features of the disease include recurrent relapse and sex and age preference, the disease pathogenesis may be partly related to epigenetic changes. However, little is known about these changes. METHODS: We analyzed genome-wide DNA methylation using the microarray-based integrated analysis of methylation by isoschizomers method...
September 15, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28915626/hdl-cholesterol-concentration-in-pregnant-chinese-han-women-of-late-second-trimester-associated-with-genetic-variants-in-cetp-abca1-apoc3-and-galnt2
#20
Mingxuan Cui, Wei Li, Liangkun Ma, Fan Ping, Juntao Liu, Xueyan Wu, Jiangfeng Mao, Xi Wang, Min Nie
OBJECTIVE: To investigate whether HDL-C level in pregnant Chinese Han women of late second trimester correlated with loci in high-density lipoprotein-cholesterol (HDL-C)-related genes found in genome-wide association studies (GWAS). METHODS: Seven single-nucleotide polymorphisms (rs3764261 in CETP, rs1532085 in LIPC, rs7241918 in LIPG, rs1883025 in ABCA1, rs4225 in APOC3, rs1059611 in LPL, and rs16851339 in GALNT2) were genotyped using the Sequenom MassArray system for 1,884 pregnant women...
August 22, 2017: Oncotarget
keyword
keyword
103416
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"